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#5226 closed defect (duplicate)

Save dialog: wrapped C/C++ object of type SaveOptionsWidget has been deleted

Reported by:	Dbarrero@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Input/Output	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-05-08)
Description
(Describe the actions that caused this problem to occur here)
Selected a chain, changed color, and clicked save 

Log:
UCSF ChimeraX version: 1.0rc202005080235 (2020-05-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/dbarrero/Desktop/dam1_phos_sites.cxs format session

Log from Fri Jul 16 09:42:07 2021UCSF ChimeraX version: 1.0rc202005080235
(2020-05-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/dbarrero/Desktop/PDB_FILES/6cfz.pdb format pdb

6cfz.pdb title:  
Structure of the dash/DAM1 complex shows its role At the yeast kinetochore-
microtubule interface [more info...]  
  
Chain information for 6cfz.pdb #1  
---  
Chain | Description  
A | DASH/DAM1 complex subunit ASK1  
B | DASH/DAM1 complex subunit DAD3  
C | DASH/DAM1 complex subunit DAD2  
D | DASH/DAM1 complex subunit DUO1  
E | DASH/DAM1 complex subunit DAD4  
F | DASH/DAM1 complex subunit DAD1  
G | DASH/DAM1 complex subunit HSK3  
H | DASH/DAM1 complex subunit DAM1  
I | DASH/DAM1 complex subunit SPC19  
J | DASH/DAM1 complex subunit SPC34  
  

> open /Users/dbarrero/Desktop/6cfz.cif

6cfz.cif title:  
Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-
microtubule interface [more info...]  
  
Chain information for 6cfz.cif #2  
---  
Chain | Description  
A | Ask1  
B | Dad3  
C | Dad2  
D | Duo1  
E | Dad4  
F | Dad1,Dad1  
G | Hsk3  
H | Dam1  
I | Spc19  
J | Spc34  
  
6cfz.cif mmCIF Assemblies  
---  
1| complete point assembly  
2| point asymmetric unit  
3| point asymmetric unit, std point frame  
  

> hide #!2 models

> show #!2 models

> hide #2.1 models

> show #2.1 models

> hide #!1 models

> sym biomt

Missing or invalid "structures" argument: invalid atomic structures specifier  

> sym #2 assembly 1

> view

> show #!1 models

> hide #2.1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> view #!1 clip false

> show #!1 cartoons

> style #!1 stick

Changed 12006 atom styles  

> hide #!1 atoms

> lighting flat

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting shadows false

> lighting full

> lighting soft

> lighting simple

> lighting soft

> select 1/B:48

Expected an objects specifier or a keyword  

> select #1/B:48

11 atoms, 10 bonds, 1 model selected  

> color sel orange red

> show sel target ab

> graphics silhouettes true

> select clear

> select #1/B:48

11 atoms, 10 bonds, 1 model selected  

> toolshed show "Color Actions"

> toolshed show "Color Actions"

> color sel byelement

> select clear

> select #1/B:52

14 atoms, 13 bonds, 1 model selected  

> color sel orange red

> toolshed show "Color Actions"

> color sel byelement

> show sel target ab

> select clear

> select #1/J:145

7 atoms, 6 bonds, 1 model selected  

> color sel orange red

> show sel target ab

> toolshed show "Color Actions"

> color sel byelement

> show sel target ab

> select #1/J:192

24 atoms, 23 bonds, 1 model selected  

> color sel orange red

> show sel target ab

> color sel byelement

> select clear

> select #1/J:199

17 atoms, 16 bonds, 1 model selected  

> color sel orange red

> show sel target ab

> color sel byelement

> select clear

> select #1/A:26

14 atoms, 13 bonds, 1 model selected  

> color sel orange red

> show sel target ab

> color sel byelement

> select clear

> view #!1 clip false

> show #!3 models

> style #!1,3 stick

Changed 24012 atom styles  

> hide #!1,3 atoms

> hide #!1,3 atoms

> show #!1,3 atoms

> show #!1,3 cartoons

> hide #!1,3 atoms

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> select #1/A:26

14 atoms, 13 bonds, 1 model selected  

> select #1/J:199

17 atoms, 16 bonds, 1 model selected  

> select #1/A:26

14 atoms, 13 bonds, 1 model selected  

> hide #!3 models

> show #!3 models

> show sel cartoons

> sym #2 assembly 1

> view

> select #1

12006 atoms, 12093 bonds, 4 pseudobonds, 2 models selected  

> ~select #1

Nothing selected  

> select #3.1

2 pseudobonds, 1 model selected  

> select #3

12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected  

> close

> open /Users/dbarrero/Desktop/6cfz.cif format mmcif

6cfz.cif title:  
Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-
microtubule interface [more info...]  
  
Chain information for 6cfz.cif #1  
---  
Chain | Description  
A | Ask1  
B | Dad3  
C | Dad2  
D | Duo1  
E | Dad4  
F | Dad1,Dad1  
G | Hsk3  
H | Dam1  
I | Spc19  
J | Spc34  
  
6cfz.cif mmCIF Assemblies  
---  
1| complete point assembly  
2| point asymmetric unit  
3| point asymmetric unit, std point frame  
  

> style stick

Changed 12006 atom styles  

> show cartoons

> hide atoms

> sym #1 assembly 1

> view

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> view #!2 clip false

> view #!2 clip false

> lighting soft

> set bgColor gray

> select #1/A:26

14 atoms, 13 bonds, 1 model selected  

> color sel orange red

> show sel target ab

> select #2

12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected  

> show #!2 models

> select #1/A:26

14 atoms, 13 bonds, 1 model selected  

> color sel red

> select #2/A:26

14 atoms, 13 bonds, 1 model selected  

> color sel orange red

> show sel target ab

> select #2/b:48

11 atoms, 10 bonds, 1 model selected  

> color sel orange red

> show sel target ab

> select #1/b:48

11 atoms, 10 bonds, 1 model selected  

> show sel target ab

> color sel orange red

> select #1/b:52

14 atoms, 13 bonds, 1 model selected  

> color sel orange red

> show sel target ab

> select #2/b:52

14 atoms, 13 bonds, 1 model selected  

> show sel target ab

> color sel orange red

> select #2/J:145

7 atoms, 6 bonds, 1 model selected  

> color sel orange red

> show sel target ab

> select #1/J:145

7 atoms, 6 bonds, 1 model selected  

> color sel orange red

> select #1/J:192

24 atoms, 23 bonds, 1 model selected  

> color sel orange red

> show sel target ab

> select #2/J:192

24 atoms, 23 bonds, 1 model selected  

> color sel orange red

> show sel target ab

> select #2/J:199

17 atoms, 16 bonds, 1 model selected  

> show sel target ab

> color sel orange red

> show sel target ab

> color sel orange red

> select #2/A:26

14 atoms, 13 bonds, 1 model selected  

> select clear

> save /Users/dbarrero/Desktop/dam1_phos_sites.cxs

opened ChimeraX session  

> hide #!2 models

> select #1

12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected  

> hide sel atoms

> color (#!1 & sel) dim gray

> set bgColor white

> select /C

2448 atoms, 2458 bonds, 2 pseudobonds, 4 models selected  

> color (#!1 & sel) cornflower blue

> select /A

2148 atoms, 2170 bonds, 2 models selected  

> toolshed show "Color Actions"

> color sel gold

> select #1

12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected  

> ~select #1

Nothing selected  

> save /Users/dbarrero/Desktop/Ian:bakerlab/Dad2_Ask1_decamer.png width 1032
> height 760 supersample 3

> toolshed show "Show Sequence Viewer"

> sequence chain #1/A #2/A

Alignment identifier is 1  

> select #1

12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected  

> toolshed show "Show Sequence Viewer"

> sequence chain #1/A #2/A

Alignment identifier is 1  

> save /Users/dbarrero/Desktop/Ian:bakerlab/Dad2_Ask1.cxs

> select #1

12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected  

> color (#!1 & sel) dark gray

> color (#!1 & sel) dim gray

> select /C

2448 atoms, 2458 bonds, 2 pseudobonds, 4 models selected  

> color (#!1 & sel) cornflower blue

> select /G

1722 atoms, 1734 bonds, 2 models selected  

> toolshed show "Color Actions"

> color sel gold

> select #1

12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected  

> ~select #1

Nothing selected  

> save /Users/dbarrero/Desktop/Ian:bakerlab/Dad2_Hsk3.cxs

> save /Users/dbarrero/Desktop/Ian:bakerlab/dad2_hsk3_decamer.jpg width 1032
> height 760 supersample 3

> select #1

12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected  

> select /G

1722 atoms, 1734 bonds, 2 models selected  

> color (#!1 & sel) dim gray

> select /I

3324 atoms, 3348 bonds, 2 models selected  

> toolshed show "Color Actions"

> color sel gold

> select #1

12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected  

> ~select #1

Nothing selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1543, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 111, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 122, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 24, in display  
self._customize_dialog(session, dialog)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 86, in _customize_dialog  
self._format_selected(session, dialog)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 98, in _format_selected  
self._options_layout.addWidget(self._current_option)  
RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted  
  
RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 98, in _format_selected  
self._options_layout.addWidget(self._current_option)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1543, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 111, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 122, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 24, in display  
self._customize_dialog(session, dialog)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 86, in _customize_dialog  
self._format_selected(session, dialog)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 98, in _format_selected  
self._options_layout.addWidget(self._current_option)  
RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted  
  
RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 98, in _format_selected  
self._options_layout.addWidget(self._current_option)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.100.362.0.0 (iBridge: 17.16.14281.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E287)
      Kernel Version: Darwin 19.4.0
      Time since boot: 16 days 13:13

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    AMD Radeon Pro 5300M:

      Chipset Model: AMD Radeon Pro 5300M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0043
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32207P1-019
      Option ROM Version: 113-D32207P1-019
      EFI Driver Version: 01.01.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2720Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: FQYMT83     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component:	Unassigned → Input/Output
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Save dialog: wrapped C/C++ object of type SaveOptionsWidget has been deleted

comment:2 by Eric Pettersen, 4 years ago

Resolution:	→ duplicate
Status:	accepted → closed

Hi Daniel,

Thanks for reporting this problem. It has been fixed in later versions so if you get ChimeraX 1.2.5 you won't run into it again. Alternatively, you could use the 'save' command directly when this happens.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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